get.scc {hicrep} | R Documentation |
calculate the stratum-adjusted correlation coefficient
get.scc(dat, resol, max)
dat |
A matrix of four columns. The first two are the mid-point coordinates of two interacting bin. |
resol |
An integer indicating the resolution of the Hi-C matrix. |
max |
An integer indicating the maximum distance of interaction that is considered. |
The function stratifies the Hi-C reads count according to their interacting distance, calculates the Pearson correlation coefficient for each stratum, then aggregrates them using a weighted average.
A list of results including stratum-specific correlation coefficients, weights, stratum-adjusted correlation coefficient (scc), and the asymptotic standard deviation of scc.
corr A vector that contains the stratum specific Pearson correlation coefficients.
wei A vector that contains the weights for each stratum.
scc Stratum-adjusted correlation coefficients.
std The asymptotic standard deviation of scc.
HiCRep: assessing the reproducibility of Hi-C data using a stratum-adjusted correlation coefficient. Tao Yang, Feipeng Zhang, Galip Gurkan Yardimci, Ross C Hardison, William Stafford Noble, Feng Yue, Qunhua Li. bioRxiv 101386; doi: https://doi.org/10.1101/101386.
data(HiCR1) data(HiCR2) processed <- prep(HiCR1, HiCR2, 1000000, 0, 5000000) scc.out = get.scc(processed, 1000000, 5000000) scc.out$scc scc.out$std